Advertisement
Table 2 Examples of bioinformatic software utilizing sketching algorithms
| Software | Purpose | Sketching algorithm |
|---|---|---|
| GROOT [25] | Variant detection in metagenomes | MinHash (KHF) |
| mashtree [26] | Phylogenetic tree construction | MinHash (KMV) |
| MashMap [27] | Long read alignment | Minimizer/MinHash (KMV) |
| MASH [1] | Sequence analysis | MinHash (KMV) |
| sourmash [22] | Sequence analysis | MinHash (KMV) |
| finch [23] | Sequence analysis | MinHash (KMV) |
| MiniMap2 [28] | Read alignment | Minimizer |
| ABySS [29] | Genome assembly | Bloom filter |
| Lighter [30] | Sequencing error correction | Bloom filter |
| BIGSI [31] | Sequence index and search | Bloom filter |
| khmer [32] | Sequence analysis | Count-Min sketch |
| FastEtch [33] | Genome assembly | Count-Min sketch |
| dashing [2] | Sequence analysis | HyperLogLog |
| krakenUniq [34] | Metagenome classification | HyperLogLog |
| HULK [4] | Sequence analysis | Histosketch |
| ntCard [35] | Sequence analysis | ntCard |
| BBsketch [24] | Sequence analysis | MinHash |
| MHAP [21] | Genome assembly | MinHash |
| MC-MinH [20] | Sequence clustering | MinHash |
| KmerGenie [36] | Sequence analysis | Count-Min sketch variant |
| Squeakr [37] | Sequence analysis | Counting Quotient Filter |
| Mantis [38] | Sequence index and search | Counting Quotient Filter |
| kssd [39] | Sequence analysis | K-mer Substring Space Decomposition |
